refactor: vg autoindex

[FelixMoelder]

The wrapper vg autoindex giraffe had to many layers. To fix this it has been moved to a more generic vg autoindex wrapper allowing to create index files for various vg subcommands. The exact workflow for which files are created for will be derived by the output file extensions set by the user. For now giraffe and map are supported as I am unaware which files will be created by rpvg and mpmap. These can be added at a later point if required.

QC

• [x] I confirm that I have followed the documentation for contributing to snakemake-wrappers.

While the contributions guidelines are more extensive, please particularly ensure that:

• [x] test.py was updated to call any added or updated example rules in a Snakefile
• [x] input: and output: file paths in the rules can be chosen arbitrarily
• [x] wherever possible, command line arguments are inferred and set automatically (e.g. based on file extensions in input: or output:)
• [x] temporary files are either written to a unique hidden folder in the working directory, or (better) stored where the Python function tempfile.gettempdir() points to
• [x] the meta.yaml contains a link to the documentation of the respective tool or command under url:
• [x] conda environments use a minimal amount of channels and packages, in recommended ordering

Summary by CodeRabbit

• New Features
  • Introduced two new rules for genome indexing: vg_autoindex_giraffe and vg_autoindex_map, enhancing workflow capabilities.
• Bug Fixes
  • Improved logic for determining workflow commands based on output file extensions.
• Tests
  • Refactored existing test function for clarity and added a new test for the vg_autoindex_map functionality.

[coderabbitai[bot]]

📝 Walkthrough

## Walkthrough This pull request involves the removal of the `vg_autoindex` rule from the `Snakefile` in the `bio/vg/autoindex/giraffe/test` directory and the addition of two new rules, `vg_autoindex_giraffe` and `vg_autoindex_map`, in the `bio/vg/autoindex/test/Snakefile`. Additionally, a new function `contains_ext` is introduced in `bio/vg/autoindex/wrapper.py` to enhance workflow command determination based on output file extensions. Changes are also made to the test structure in `test_wrappers.py` to improve clarity and coverage. ## Changes | File Path | Change Summary | |-----------------------------------------|---------------------------------------------------------------------------------------------------------| | bio/vg/autoindex/giraffe/test/Snakefile | Rule removed: `vg_autoindex` | | bio/vg/autoindex/test/Snakefile | Rules added: `vg_autoindex_giraffe`, `vg_autoindex_map` | | bio/vg/autoindex/wrapper.py | Function added: `def contains_ext(extensions)` | | test_wrappers.py | Function signature updated: `test_vg_autoindex_giraffe` renamed to `test_vg_autoindex`; New method added: `test_vg_autoindex_map` | ## Possibly related PRs - **#3452**: The main PR removes the `vg_autoindex` rule from the `Snakefile`, while this retrieved PR introduces a new `vg_autoindex` rule in a different context, specifically for the Giraffe tool, indicating a direct relationship in terms of functionality and naming. ## Suggested reviewers - fgvieira - johanneskoester

[!WARNING]

Rate limit exceeded

@FelixMoelder has exceeded the limit for the number of commits or files that can be reviewed per hour. Please wait 18 minutes and 46 seconds before requesting another review.

⌛ How to resolve this issue?

After the wait time has elapsed, a review can be triggered using the `@coderabbitai review` command as a PR comment. Alternatively, push new commits to this PR. We recommend that you space out your commits to avoid hitting the rate limit.

🚦 How do rate limits work?

CodeRabbit enforces hourly rate limits for each developer per organization. Our paid plans have higher rate limits than the trial, open-source and free plans. In all cases, we re-allow further reviews after a brief timeout. Please see our [FAQ](https://docs.coderabbit.ai/faq) for further information.

📥 Commits

Reviewing files that changed from the base of the PR and between 722f872d92e0a5003a141dda499df4ff8d8d9942 and 4a443a85b91934e0f5249ccb95d2836bfe7c30fa.

---

Thank you for using CodeRabbit. We offer it for free to the OSS community and would appreciate your support in helping us grow. If you find it useful, would you consider giving us a shout-out on your favorite social media?

❤️ Share

- [X](https://twitter.com/intent/tweet?text=I%20just%20used%20%40coderabbitai%20for%20my%20code%20review%2C%20and%20it%27s%20fantastic%21%20It%27s%20free%20for%20OSS%20and%20offers%20a%20free%20trial%20for%20the%20proprietary%20code.%20Check%20it%20out%3A&url=https%3A//coderabbit.ai) - [Mastodon](https://mastodon.social/share?text=I%20just%20used%20%40coderabbitai%20for%20my%20code%20review%2C%20and%20it%27s%20fantastic%21%20It%27s%20free%20for%20OSS%20and%20offers%20a%20free%20trial%20for%20the%20proprietary%20code.%20Check%20it%20out%3A%20https%3A%2F%2Fcoderabbit.ai) - [Reddit](https://www.reddit.com/submit?title=Great%20tool%20for%20code%20review%20-%20CodeRabbit&text=I%20just%20used%20CodeRabbit%20for%20my%20code%20review%2C%20and%20it%27s%20fantastic%21%20It%27s%20free%20for%20OSS%20and%20offers%20a%20free%20trial%20for%20proprietary%20code.%20Check%20it%20out%3A%20https%3A//coderabbit.ai) - [LinkedIn](https://www.linkedin.com/sharing/share-offsite/?url=https%3A%2F%2Fcoderabbit.ai&mini=true&title=Great%20tool%20for%20code%20review%20-%20CodeRabbit&summary=I%20just%20used%20CodeRabbit%20for%20my%20code%20review%2C%20and%20it%27s%20fantastic%21%20It%27s%20free%20for%20OSS%20and%20offers%20a%20free%20trial%20for%20proprietary%20code)

🪧 Tips

### Chat There are 3 ways to chat with [CodeRabbit](https://coderabbit.ai): - Review comments: Directly reply to a review comment made by CodeRabbit. Example: - `I pushed a fix in commit , please review it.` - `Generate unit testing code for this file.` - `Open a follow-up GitHub issue for this discussion.` - Files and specific lines of code (under the "Files changed" tab): Tag `@coderabbitai` in a new review comment at the desired location with your query. Examples: - `@coderabbitai generate unit testing code for this file.` - `@coderabbitai modularize this function.` - PR comments: Tag `@coderabbitai` in a new PR comment to ask questions about the PR branch. For the best results, please provide a very specific query, as very limited context is provided in this mode. Examples: - `@coderabbitai gather interesting stats about this repository and render them as a table. Additionally, render a pie chart showing the language distribution in the codebase.` - `@coderabbitai read src/utils.ts and generate unit testing code.` - `@coderabbitai read the files in the src/scheduler package and generate a class diagram using mermaid and a README in the markdown format.` - `@coderabbitai help me debug CodeRabbit configuration file.` Note: Be mindful of the bot's finite context window. It's strongly recommended to break down tasks such as reading entire modules into smaller chunks. For a focused discussion, use review comments to chat about specific files and their changes, instead of using the PR comments. ### CodeRabbit Commands (Invoked using PR comments) - `@coderabbitai pause` to pause the reviews on a PR. - `@coderabbitai resume` to resume the paused reviews. - `@coderabbitai review` to trigger an incremental review. This is useful when automatic reviews are disabled for the repository. - `@coderabbitai full review` to do a full review from scratch and review all the files again. - `@coderabbitai summary` to regenerate the summary of the PR. - `@coderabbitai resolve` resolve all the CodeRabbit review comments. - `@coderabbitai configuration` to show the current CodeRabbit configuration for the repository. - `@coderabbitai help` to get help. ### Other keywords and placeholders - Add `@coderabbitai ignore` anywhere in the PR description to prevent this PR from being reviewed. - Add `@coderabbitai summary` to generate the high-level summary at a specific location in the PR description. - Add `@coderabbitai` anywhere in the PR title to generate the title automatically. ### CodeRabbit Configuration File (`.coderabbit.yaml`) - You can programmatically configure CodeRabbit by adding a `.coderabbit.yaml` file to the root of your repository. - Please see the [configuration documentation](https://docs.coderabbit.ai/guides/configure-coderabbit) for more information. - If your editor has YAML language server enabled, you can add the path at the top of this file to enable auto-completion and validation: `# yaml-language-server: $schema=https://coderabbit.ai/integrations/schema.v2.json` ### Documentation and Community - Visit our [Documentation](https://docs.coderabbit.ai) for detailed information on how to use CodeRabbit. - Join our [Discord Community](http://discord.gg/coderabbit) to get help, request features, and share feedback. - Follow us on [X/Twitter](https://twitter.com/coderabbitai) for updates and announcements.